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#+title: Updates on open research

#+date: <2018-04-29>

It has been 9 months since I last wrote about open (maths) research.
Since then two things happened which prompted me to write an update.

As always I discuss open research only in mathematics, not because I
think it should not be applied to other disciplines, but simply because
I do not have experience nor sufficient interests in non-mathematical
subjects.

First, I read about Richard Stallman the founder of the free software
movement, in [[http://shop.oreilly.com/product/9780596002879.do][his
biography by Sam Williams]] and his own collection of essays
[[https://shop.fsf.org/books-docs/free-software-free-society-selected-essays-richard-m-stallman-3rd-edition][/Free
software, free society/]], from which I learned a bit more about the
context and philosophy of free software and its relation to that of open
source software. For anyone interested in open research, I highly
recommend having a look at these two books. I am also reading Levy's
[[http://www.stevenlevy.com/index.php/books/hackers][Hackers]], which
documented the development of the hacker culture predating Stallman. I
can see the connection of ideas from the hacker ethic to the free
software philosophy and to the open source philosophy. My guess is that
the software world is fortunate to have pioneers who advocated for
various kinds of freedom and openness from the beginning, whereas for
academia which has a much longer history, credit protection has always
been a bigger concern.

Also a month ago I attended a workshop called
[[https://www.perimeterinstitute.ca/conferences/open-research-rethinking-scientific-collaboration][Open
research: rethinking scientific collaboration]]. That was the first time
I met a group of people (mostly physicists) who also want open research
to happen, and we had some stimulating discussions. Many thanks to the
organisers at Perimeter Institute for organising the event, and special
thanks to
[[https://www.perimeterinstitute.ca/people/matteo-smerlak][Matteo
Smerlak]] and
[[https://www.perimeterinstitute.ca/people/ashley-milsted][Ashley
Milsted]] for invitation and hosting.

From both of these I feel like I should write an updated post on open
research.

*** Freedom and community
    :PROPERTIES:
    :CUSTOM_ID: freedom-and-community
    :ID:       f0ec8170-e86e-49c6-bd34-3904f31317eb
    :END:
Ideals matter. Stallman's struggles stemmed from the frustration of
denied request of source code (a frustration I shared in academia except
source code is replaced by maths knowledge), and revolved around two
things that underlie the free software movement: freedom and community.
That is, the freedom to use, modify and share a work, and by sharing, to
help the community.

Likewise, as for open research, apart from the utilitarian view that
open research is more efficient / harder for credit theft, we should not
ignore the ethical aspect that open research is right and fair. In
particular, I think freedom and community can also serve as principles
in open research. One way to make this argument more concrete is to
describe what I feel are the central problems: NDAs (non-disclosure
agreements) and reproducibility.

*NDAs*. It is assumed that when establishing a research collaboration,
or just having a discussion, all those involved own the joint work in
progress, and no one has the freedom to disclose any information
e.g. intermediate results without getting permission from all
collaborators. In effect this amounts to signing an NDA. NDAs are
harmful because they restrict people's freedom from sharing information
that can benefit their own or others' research. Considering that in
contrast to the private sector, the primary goal of academia is
knowledge but not profit, NDAs in research are unacceptable.

*Reproducibility*. Research papers written down are not necessarily
reproducible, even though they appear on peer-reviewed journals. This is
because the peer-review process is opaque and the proofs in the papers
may not be clear to everyone. To make things worse, there are no open
channels to discuss results in these papers and one may have to rely on
interacting with the small circle of the informed. One example is folk
theorems. Another is trade secrets required to decipher published works.

I should clarify that freedom works both ways. One should have the
freedom to disclose maths knowledge, but they should also be free to
withhold any information that does not hamper the reproducibility of
published works (e.g. results in ongoing research yet to be published),
even though it may not be nice to do so when such information can help
others with their research.

Similar to the solution offered by the free software movement, we need a
community that promotes and respects free flow of maths knowledge, in
the spirit of the [[https://www.gnu.org/philosophy/][four essential
freedoms]], a community that rejects NDAs and upholds reproducibility.

Here are some ideas on how to tackle these two problems and build the
community:

1. Free licensing. It solves NDA problem - free licenses permit
   redistribution and modification of works, so if you adopt them in
   your joint work, then you have the freedom to modify and distribute
   the work; it also helps with reproducibility - if a paper is not
   clear, anyone can write their own version and publish it. Bonus
   points with the use of copyleft licenses like
   [[https://creativecommons.org/licenses/by-sa/4.0/][Creative Commons
   Share-Alike]] or the [[https://www.gnu.org/licenses/fdl.html][GNU
   Free Documentation License]].
2. A forum for discussions of mathematics. It helps solve the
   reproducibility problem - public interaction may help quickly clarify
   problems. By the way, Math Overflow is not a forum.
3. An infrastructure of mathematical knowledge. Like the GNU system, a
   mathematics encyclopedia under a copyleft license maintained in the
   Github-style rather than Wikipedia-style by a "Free Mathematics
   Foundation", and drawing contributions from the public (inside or
   outside of the academia). To begin with, crowd-source (again,
   Github-style) the proofs of say 1000 foundational theorems covered in
   the curriculum of a bachelor's degree. Perhaps start with taking
   contributions from people with some credentials (e.g. having a
   bachelor degree in maths) and then expand the contribution permission
   to the public, or taking advantage of existing corpus under free
   license like Wikipedia.
4. Citing with care: if a work is considered authorative but you
   couldn't reproduce the results, whereas another paper which tries to
   explain or discuss similar results makes the first paper
   understandable to you, give both papers due attribution (something
   like: see [1], but I couldn't reproduce the proof in [1], and the
   proofs in [2] helped clarify it). No one should be offended if you
   say you can not reproduce something - there may be causes on both
   sides, whereas citing [2] is fairer and helps readers with a similar
   background.

*** Tools for open research
    :PROPERTIES:
    :CUSTOM_ID: tools-for-open-research
    :ID:       07f852e1-c95d-407f-972b-8395ac7903a4
    :END:
The open research workshop revolved around how to lead academia towards
a more open culture. There were discussions on open research tools,
improving credit attributions, the peer-review process and the path to
adoption.

During the workshop many efforts for open research were mentioned, and
afterwards I was also made aware by more of them, like the following:

- [[https://osf.io][OSF]], an online research platform. It has a clean
  and simple interface with commenting, wiki, citation generation, DOI
  generation, tags, license generation etc. Like Github it supports
  private and public repositories (but defaults to private), version
  control, with the ability to fork or bookmark a project.
- [[https://scipost.org/][SciPost]], physics journals whose peer review
  reports and responses are public (peer-witnessed refereeing), and
  allows comments (post-publication evaluation). Like arXiv, it requires
  some academic credential (PhD or above) to register.
- [[https://knowen.org/][Knowen]], a platform to organise knowledge in
  directed acyclic graphs. Could be useful for building the
  infrastructure of mathematical knowledge.
- [[https://fermatslibrary.com/][Fermat's Library]], the journal club
  website that crowd-annotates one notable paper per week released a
  Chrome extension [[https://fermatslibrary.com/librarian][Librarian]]
  that overlays a commenting interface on arXiv. As an example Ian
  Goodfellow did an
  [[https://fermatslibrary.com/arxiv_comments?url=https://arxiv.org/pdf/1406.2661.pdf][AMA
  (ask me anything) on his GAN paper]].
- [[https://polymathprojects.org/][The Polymath project]], the famous
  massive collaborative mathematical project. Not exactly new, the
  Polymath project is the only open maths research project that has
  gained some traction and recognition. However, it does not have many
  active projects
  ([[http://michaelnielsen.org/polymath1/index.php?title=Main_Page][currently
  only one active project]]).
- [[https://stacks.math.columbia.edu/][The Stacks Project]]. I was made
  aware of this project by [[https://people.kth.se/~yitingl/][Yiting]].
  Its data is hosted on github and accepts contributions via pull
  requests and is licensed under the GNU Free Documentation License,
  ticking many boxes of the free and open source model.

*** An anecdote from the workshop
    :PROPERTIES:
    :CUSTOM_ID: an-anecdote-from-the-workshop
    :ID:       857899dd-f3f8-4eac-a14a-779604066da4
    :END:
In a conversation during the workshop, one of the participants called
open science "normal science", because reproducibility, open access,
collaborations, and fair attributions are all what science is supposed
to be, and practices like treating the readers as buyers rather than
users should be called "bad science", rather than "closed science".

To which an organiser replied: maybe we should rename the workshop
"Not-bad science".
